Bastille-Rousseau G, Yackulic C, Frair J, Cabrera F, Blake S.2016. Allometric and temporal scaling of movement characteristics in Galapagos tortoises. Journal of Animal Ecology 85(5): 1171–1181. https://doi.org/10.1111/1365-2656.12561
# ggplot() +
# geom_point(data=data,aes(location.long,location.lat,color=individual.local.identifier)) +
# labs(x="Longitude", y="Latitude") +
# guides(color=guide_legend("Identifier"))
lapply(split(data, data$individual.local.identifier),
function(x)write.csv(x, file = paste(x$individual.local.identifier[1],".csv"), row.names = FALSE))
## $`Freddy V`
## NULL
##
## $Mary
## NULL
##
## $Nigel
## NULL
files <- list.files(path = ".", pattern = " .*\\.csv", full.names = TRUE)
utm_points <- cbind(data$utm.easting, data$utm.northing)
utm_locations <- SpatialPoints(utm_points,
proj4string=CRS("+proj=utm +zone=15 +south +datum=WGS84"))
proj_lat.lon <- as.data.frame(spTransform(
utm_locations, CRS("+proj=longlat +datum=WGS84")))
colnames(proj_lat.lon) <- c("x","y")
raster <- openmap(c(max(proj_lat.lon$y)+0.01, min(proj_lat.lon$x)-0.01),
c(min(proj_lat.lon$y)-0.01, max(proj_lat.lon$x)+0.01),
type = "bing")
raster_utm <- openproj(raster,
projection = "+proj=utm +zone=15 +south +ellps=WGS84 +units=m +no_defs")
autoplot(raster_utm, expand = TRUE) + theme_bw() +
theme(legend.position="bottom") +
theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
geom_point(data=data, aes(utm.easting,
utm.northing,
color=individual.local.identifier), size = 3, alpha = 0.8) +
theme(axis.title = element_text(face="bold")) + labs(x="Easting",
y="Northing") +
guides(color=guide_legend("Identifier"))
mcp_raster <- function(filename){
data <- read.csv(file = filename)
x <- as.data.frame(data$utm.easting)
y <- as.data.frame(data$utm.northing)
xy <- c(x,y)
data.proj <- SpatialPointsDataFrame(xy,data, proj4string = CRS("+proj=utm +zone=15 +south +ellps=WGS84 +units=m +no_defs"))
xy <- SpatialPoints(data.proj@coords)
mcp.out <- mcp(xy, percent=100, unout="ha")
mcp.points <- cbind((data.frame(xy)),data$individual.local.identifier)
colnames(mcp.points) <- c("x","y", "identifier")
mcp.poly <- fortify(mcp.out, region = "id")
units <- grid.text(paste(round(mcp.out@data$area,2),"ha"), x=0.85, y=0.95,
gp=gpar(fontface=4, col="white", cex=0.9), draw = FALSE)
mcp.plot <- autoplot(raster_utm, expand = TRUE) + theme_bw() + theme(legend.position="none") +
theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
geom_polygon(data=mcp.poly, aes(x=mcp.poly$long, y=mcp.poly$lat), alpha = 0.4, fill="orange") +
geom_point(data=mcp.points, aes(x=x, y=y)) +
labs(x="Easting (m)", y="Northing (m)", title=mcp.points$identifier) +
theme(legend.position="none", plot.title = element_text(face = "bold", hjust = 0.5)) +
annotation_custom(units)
mcp.plot
}
pblapply(files, mcp_raster)
## [[1]]
##
## [[2]]
##
## [[3]]
kde_raster <- function(filename){
data <- read.csv(file = filename)
x <- as.data.frame(data$utm.easting)
y <- as.data.frame(data$utm.northing)
xy <- c(x,y)
data.proj <- SpatialPointsDataFrame(xy,data, proj4string = CRS("+proj=utm +zone=15 +south +ellps=WGS84 +units=m +no_defs"))
xy <- SpatialPoints(data.proj@coords)
kde<-kernelUD(xy, h="href", kern="bivnorm", grid=100)
ver <- getverticeshr(kde, 95)
kde.points <- cbind((data.frame(data.proj@coords)),data$individual.local.identifier)
colnames(kde.points) <- c("x","y","identifier")
kde.poly <- fortify(ver, region = "id")
units <- grid.text(paste(round(ver$area,2)," ha"), x=0.85, y=0.95,
gp=gpar(fontface=4, col="white", cex=0.9), draw = FALSE)
kde.plot <- autoplot(raster_utm, expand = TRUE) + theme_bw() + theme(legend.position="none") +
theme(panel.border = element_rect(colour = "black", fill=NA, size=1)) +
geom_polygon(data=kde.poly, aes(x=kde.poly$long, y=kde.poly$lat), alpha = 0.4, fill="orange") +
geom_point(data=kde.points, aes(x=x, y=y)) +
labs(x="Easting (m)", y="Northing (m)", title=kde.points$identifier) +
theme(legend.position="none", plot.title = element_text(face = "bold", hjust = 0.5)) +
annotation_custom(units)
kde.plot
}
pblapply(files, kde_raster)
## [[1]]
##
## [[2]]
##
## [[3]]